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║ Biologist-Biotechnologist | Postdoc | Liquid Biopsy Specialist ║
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About Me
I’m a postdoctoral researcher at the Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, specialising in liquid biopsy development and circulating cell-free DNA analysis. My work combines long-read and short-read sequencing technologies with computational biology to develop novel diagnostic tools for metabolic disorders and obesity-related diseases.
┌─────────────────────────────────────────────────────────────┐
│ RESEARCH FOCUS │
├─────────────────────────────────────────────────────────────┤
│ → Liquid biopsy development │
│ → Cell-free DNA biology and diagnostics │
│ → Long-read and short-read sequencing │
│ → Epigenetic biomarkers in metabolic disease │
│ → Machine learning for clinical applications │
└─────────────────────────────────────────────────────────────┘
Current Projects
MethylSense: ML-Powered cfDNA Methylation Diagnostics
[In Development]
Building machine learning models that leverage cell-free DNA methylation patterns from nanopore sequencing for disease prediction and clinical decision support in metabolic disorders. Based on recent research demonstrating the diagnostic potential of cfDNA methylation profiling in obesity and related conditions.
Preprint: bioRxiv 2025.04.11.648151
NanoporeToBED Pipeline
[Nanopore Data] → [Processing] → [BED Format] → [Downstream Analysis]
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Raw FAST5 Basecalling Methylation Visualisation
Raw POD5 Alignment Modification Statistical
QC Steps Calling Analysis
github.com/markusdrag/NanoporeToBED-Pipeline
A streamlined bioinformatics workflow for converting nanopore sequencing data into analysis-ready BED format for epigenetic studies.
GenomeToWindows
[Ensembl/UCSC] → [Download] → [Index] → [Window] → [BED Output]
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Genome DBs Auto-detect samtools bedtools Custom sizes
100+ spp. Latest faidx makewindows (1-25kb)
github.com/markusdrag/GenomeToWindows
Automated genome downloading and windowing tool for MethylSense preprocessing. Downloads genomes from Ensembl or UCSC and generates genomic windows with flexible sizes (1kb-25kb). Features automatic fallback between databases, progress tracking, dry-run mode, and automated environment setup.
Key Features:
- Supports 100+ species from Ensembl and UCSC
- Automatic genome downloading and indexing
- Flexible window sizes with sensible defaults
- Database fallback for robust operation
- One-command installation with micromamba/conda
Tech Stack
┌──────────────────┬──────────────────────────────────────────────┐
│ Languages │ R, Bash, Python │
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│ Workflows │ Nextflow, Shell scripting │
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│ Nanopore Tools │ Dorado, Modkit, Minimap2, Samtools │
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│ R Packages │ ggplot2, dplyr, tidyverse, DESeq2 │
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│ Stat Genetics │ PLINK, Matrix eQTL, FastQTL │
├──────────────────┼──────────────────────────────────────────────┤
│ Infrastructure │ HPC environments, Linux, Git │
└──────────────────┴──────────────────────────────────────────────┘
Selected Publications & Research
Google Scholar: Markus H. Drag
Selected publications:
Liquid Biopsy & cfDNA:
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Drag MH et al. (2023). Nanopore sequencing reveals methylation changes associated with obesity in circulating cell-free DNA from Göttingen Minipigs. Epigenetics, 18(1):1. doi:10.1080/15592294.2023.2199374
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Drag MH & Kilpeläinen TO (2021). Cell-Free DNA and RNA—Measurement and Applications in Clinical Diagnostics with Focus on Metabolic Disorders. Physiol Genomics, 53:33-46. doi:10.1152/physiolgenomics.00086.2020
Systems Genomics & eQTLs:
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Drag MH et al. (2019). Characterisation of eQTLs Associated with Androstenone by RNA Sequencing in Porcine Testis. Physiol Genomics, 51:488-499. doi:10.1152/physiolgenomics.00125.2018
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Drag MH et al. (2018). Systems Genomics Study Reveals Expression Quantitative Trait Loci, Regulator Genes and Pathways Associated with Boar Taint in Pigs. PLoS One, 13(2):e0192673. doi:10.1371/journal.pone.0192673
Transcriptomics:
- Drag MH et al. (2017). Differential Expression and Co-Expression Gene Networks Reveal Candidate Biomarkers of Boar Taint in Non-Castrated Pigs. Sci Rep, 7:12205. doi:10.1038/s41598-017-11928-0
Let’s Connect
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│ LinkedIn: linkedin.com/in/markusdrag │
│ Scholar: scholar.google.com/citations?user=KHoAwvoAAAAJ│
│ Email: markus.drag@sund.ku.dk │
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"From each cfDNA fragment to biological insight—one methylation mark at a time"